Additional file 2 of Phosphoproteomics of short-term hedgehog signaling in human medulloblastoma cells
Bibliographic record
Abstract
Additional file 1: Table S-1. Eluent B (B) gradient range and gradient duration for the different analyzed fractions. Table S-2. Applied R-packages. Responsiveness of DAOY cells to SAG and vismodegib treatment. RNA isolation and quantitative PCR (qPCR). Table S-3. Primer Sequences used for qPCR. Figure S-1. Hedgehog target gene expression in SAG and vismodegib treated DAOY cells. Figure S-2. Comparable Hedgehog pathway induction by natural and synthetic HH pathway activators. Figure S-3. Distribution of protein groups identified after 5.0 min treatment (A) and 15 min treatment (B). Figure S-4. Ingenuity pathway analysis of all phosphopeptides identified after 15 min using a phosphorylation analysis. Figure S-5. Time dependent Ingenuity pathway analysis of cancer associated pathways. Figure S-6. Western blot validation of PKA activity modulation in response to SMO agonist and antagonists. Table S-4. Antibodies used for Western blot analysis. Figure S-7. Overlap of quantified phosphopeptides after 5.0 and 15 min. Figure S-8. Volcano plots of phosphopeptides identified after 5.0 min treatment. Figure S-9. Kinase substrate enrichment analysis (KSEA) was performed for phosphopeptides identified after 5.0 min treatment for the ratio SAG/Vismo using the online platform KSEA App (https://casecpb.shinyapps.io/ksea/). Figure S-10. Volcano plots and kinase set enrichment analysis for phosphopeptides identified after 15 min treatment. Figure S-11. IFT172 phosphorylation and expression after 5.0 and 15 min.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.733 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".